Analysis of transcription factory and epigenomic modification in inflammatory stimulation driven transcription wave

内皮细胞的慢性炎症是动脉粥样硬化形成的第一阶段。我们应用了一个实验模型，使用内皮细胞与代表性的炎症刺激剂，肿瘤坏死因子-α（TNFα），并剖析了详细的机制，诱导和减少超过500个基因。为了全面了解TNFα引起的单个转录周期的时间进程，我们用TNFα打开了5个长（>100 kbp）基因，并监测了新生RNA、RNA Pol II、绝缘子和组蛋白修饰的基因组定位。激活触发了一波转录，沿着沿着基因横扫，Pol II倾向于在粘附素/CTCF结合位点停滞。染色质构象捕获（3C），无论是传统的和定量的数据，揭示了共定位的积极转录的基因。这些结果表明，TNFα应答基因的微调是通过选择数量的转录复合物来实现的，这些转录复合物为转录和剪接提供了平台。利用全基因组染色质相互作用分析和配对末端标签测序（ChIA-PET）技术，可以对染色质结构进行详细的分析，刺激内皮细胞的时程数据揭示了半小时内染色质结构的动态变化。

Chronic inflammation of endothelial cell is the first stage ofatherogenesis. We applied an experimental model using endothelial cells with representative inflammatory stimulant, tumor necrosis factor-alpha (TNFα), and to dissect detailedmechanism of induction and reduction of more than 500 genes. To obtain a comprehensive view of a single transcription cycle caused by TNFα in time course manner, we switched onfive long (>100 kbp) genes with TNFα and monitored genomic localization of nascent RNA, RNA Pol II, insulators, and histone modifications. Activation triggers a wave of transcriptionthat sweeps along the genes, and Pol II tends to stall at cohesin/CTCF binding sites. Chromatin conformation capture (3C), both conventional and quantitative data, revealedco-localization of actively transcribed genes. These results suggested that fine-tuning of TNFα responsive genes is achieved by selected number of transcription complexes, whichprovide platform for both transcription and splic ng. By virtue of whole genome chromatininteraction analysis with paired end tag sequencing (ChIA-PET) detailed chromatin structureanalysis was made possible, and time course data on stimulated endothelium sheds light ondynamic chromatin structure change within half an hour.